Five Days in Madrid: EAT!!!
Seriously, though...obviously spend some QUALITY time in the Prado. I'm a huge El Greco fan as well as Goya (pinturas negras are not to be missed...ask someone how they got there...great story!). The Prado blows doors off of the Louvre, and the paintings are all legitimate, not stolen art!!!
One place that most haven't mentioned here is the Museo Arqueológico just up the street from the Puerta de Alcalá. There you'll find some of the physical artefacts that represent the millenia of history in Iberia. La Dama de Elche is there, some funky Visigothic royal jewels, etc. There's even a complete recreation of la cueva de Altamira. In an afternoon, you can flow through the history of Spain and really get a feel for the city and country you're visiting. You can follow that up with some people-watching in the Retiro while you chow on some good Spanish food!
As was mentioned, with five days, you may want to break up the trip on day three and take a day trip to Segovia...MUCH to see there. (You can't miss with Toledo either, but I have a Segovia bias,
sorry!)
Regardless of what you decide, you will definitely enjoy...don't forget to tell us all about it!!!